MolNFT v1 · #179098 · protein

Human CD73 (ecto 5'-nucleotidase) in complex with compound 35

7JV8: “Human CD73 (ecto 5'-nucleotidase) in complex with compound 35”. X-ray diffraction, 3 ligands (VPD, ZN, CA), 18 pockets (best druggability 0.85). MolNFT v1 #179098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JV8
Type: protein
Length: 2,097 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-nucleotidase
EC: 3.1.3.5
UniProt: P21589
Ligands: VPD, ZN, CA
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	5'-nucleotidase (EC 3.1.3.5)	protein	525	30% helix, 26% strand	P21589
B	5'-nucleotidase (EC 3.1.3.5)	protein	518	30% helix, 27% strand	P21589
C	5'-nucleotidase (EC 3.1.3.5)	protein	529	30% helix, 27% strand	P21589

Ligands and binding sites

VPD · 6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	852	0.85	0.87	93	empty
2	733	0.84	0.87	76	empty
3	952	0.80	0.82	118	VPD
4	644	0.76	0.82	81	VPD
5	664	0.76	0.82	82	VPD

Interfaces

5 interfaces between chains.

A–D · 1479 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1218 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 424 Å² buried · 1 hydrogen bond · protein-protein
B–D · 268 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 249 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

7JV8 · Human CD73 (ecto 5'-nucleotidase) in complex with compound 35 · the same entry in another collection · chain D against D, TM-score 1.00
P21589 · AlphaFold monomer V2.0 prediction for 5'-nucleotidase (P21589) · a predicted model of the same protein · chain D against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P21589
Elsewhere: RCSB PDB 7JV8 · PDBe 7JV8 · UniProt P21589

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